[Mister Pontiac]

Wow, Joe. So sorry to read about this after all you've been thru.

I'll offer up my advice. Of course it's only that, my advice, so feel free to take it or leave it. But if I were in your shoes, this is how I would proceed...

First off, Paul has been thru the motor twice, and has discovered nothing catastrophic going on inside. Those bases have been covered.

Second, since the same sound was not heard 'consistently' when the engine was out of the car, but has been heard "rhythmically" both before and after only when the engine is in the car, it seems to indicate the noise may be related to another part of the drivetrain. I know you have been thru the flex plate/converter bolt scenario and there is nothing wrong there. So while the culprit is still at large, you have eliminated another potential drivetrain problem there too.

At this point, knowing these things, I would absolutely drive the car. A lot in fact. I would take it somewhat easy in the beginning, monitor the vitals (water temp, oil psi), and as you go, listen each time for the sound after you drive. If in fact you do have a mechanical issue where metal to metal contact is occurring, it should lessen as you drive as the problem continues to 'self clearance.' If however that's not what is happening, and you do have a failure looming (like a bearing or what have you), the noise will likely get worse as you drive.

So don't be afraid of it. Drive it. Just don't hammer on it too hard for a while until you decide if the noise is slowly going away, slowly getting louder, or simply staying the same. Based on those results, the diagnosis will likely get easier.

The hardest problems to diagnose are always the "almost broken" problems.

Hope that helps some, and like the others, I'll be waiting to hear how things progress.